The fitness cost of the genes responsible for resistance to fluoroquinolones in clinical isolates of Streptococcus pneumoniae were estimated in vitro in a common genetic background. Naturally occurring parC, parE, and gyrA loci containing mutations in the quinolone-resistance-determining regions were introduced by transformation into S. pneumoniae strain R6 individually and in combinations. The fitness of these transformants was estimated by pairwise competition experiments with a common R6 strain. On average, single par and gyr mutants responsible for low-level MIC resistance (first-step resistance) impose a fitness burden of approximately 8%. Some of these mutants engender no measurable cost, while one, a parE mutant, reduces the fitness of these bacteria by more than 40%. Most interestingly, the addition of the second par or gyr mutations required for clinically significant, high-MIC fluoroquinolone resistance does not increase the fitness burden imposed by these single genes and can even reduce it. We discuss the implications of these results for the epidemiology of fluoroquinolone resistance and the evolution of acquired resistance in treated patients.Streptococcus pneumoniae remains a leading cause of invasive bacterial diseases such as pneumonia, meningitis, and sepsis and is the most significant cause of acute otitis media in children, accounting for between 5 and 7 million otitis media cases annually in the United States alone (9, 48). While in the past, these infections were effectively treated with beta-lactam antibiotics including penicillin, in part due to the rising frequency of resistance to these compounds (32, 37, 45), other classes of antimicrobial agents are increasingly being employed to treat pneumococcal disease. Of these, the fluoroquinolones have been particularly successful for treating pneumococcal infections in adults (30).Unfortunately, as observed for antimicrobial agents of other classes, S. pneumoniae strains with high-MIC resistance to fluoroquinolones (FQs) have emerged (1,7,31,51) and lead to a number of reported instances of FQ treatment failure (11,13,41). Although the frequency of clinical isolates of S. pneumoniae with high-MIC resistance to FQ remains low and appears to have leveled off at ϳ3% for isolates within North America (28-30, 42), it is not clear if this frequency has genuinely plateaued or if it will continue to rise with increasing FQ use. This concern is particularly heightened by proposals to recommend FQs for a broader range of indications and for children, for which and for whom they are not currently employed (1).In theory, whether or not the frequency of resistance to FQs or any other antimicrobial agent will increase, and the rate of that increase, will be directly proportional to the efficacy of the antimicrobial and the extent of its use and inversely proportional to the cost that resistance imposes on bacterial fitness (3,25). In compartment models of antimicrobial treatment, the fitness of a bacterial strain is directly proportional to its rate of infe...